Files in arendsee/synder
Use Synteny to Filter Genomic Search
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
FUNDING
LICENSE
NAMESPACE
R/RcppExports.R
R/cast.R
R/classes.R
R/data.R
R/interpret.R
R/plot.R
R/print.R
R/read.R
R/relate.R
R/rsynder.R
R/types.R
R/util.R
README.md
TODO
codecov.yml
data/intro_1.rda
data/intro_2.rda
data/toy.rda
data/ty1.rda
inst/CITATION
inst/arabidopsis/al.gff
inst/arabidopsis/at-vs-al.syn
inst/arabidopsis/at.gff
inst/arabidopsis/nfyc_at-vs-al_blastp.tab
inst/arabidopsis/nfyc_at-vs-al_tblastn.tab
man/anon_search.Rd
man/as_conlen.Rd
man/as_gff.Rd
man/as_synmap.Rd
man/c_count.Rd
man/c_dump.Rd
man/c_filter.Rd
man/c_map.Rd
man/c_search.Rd
man/dot-overlaps.Rd
man/featureMap.Rd
man/flag_summary.Rd
man/intro_1.Rd
man/intro_2.Rd
man/is_incoherent.Rd
man/is_unassembled.Rd
man/load_blastp_file.Rd
man/load_tblastn_file.Rd
man/make_blastp_map.Rd
man/make_tblastn_gene_map.Rd
man/make_tblastn_si_map.Rd
man/neighborhood_madness.Rd
man/plot.DumpResult.Rd
man/plot.SearchResult.Rd
man/plot.Synmap.Rd
man/synder.Rd
man/synder_cast.Rd
man/synder_classes.Rd
man/synder_commands.Rd
man/synder_print.Rd
man/synder_read.Rd
man/syntenic_density.Rd
man/syntenic_scatter.Rd
man/toy.Rd
man/ty1.Rd
src/.gitignore
src/RcppExports.cpp
src/block.cpp
src/block.h
src/bound.cpp
src/bound.h
src/contig.cpp
src/contig.h
src/contiguous_set.cpp
src/contiguous_set.h
src/feature.h
src/genome.cpp
src/genome.h
src/global.h
src/interval.h
src/interval_result.h
src/interval_set.h
src/interval_tree.h
src/linked_interval.h
src/many_blocks.cpp
src/many_blocks.h
src/many_contiguous_sets.cpp
src/many_contiguous_sets.h
src/rsynder.cpp
src/search_interval.cpp
src/search_interval.h
src/synmap.cpp
src/synmap.h
src/types.cpp
src/types.h
tests/testthat.R
tests/testthat/deletion/between-exp.txt
tests/testthat/deletion/between.gff
tests/testthat/deletion/map.syn
tests/testthat/interruptions/multi-chromosome/between-exp.txt
tests/testthat/interruptions/multi-chromosome/between.gff
tests/testthat/interruptions/multi-chromosome/map.syn
tests/testthat/interruptions/nested/between-exp.txt
tests/testthat/interruptions/nested/between-k3-exp.txt
tests/testthat/interruptions/nested/between-k4-exp.txt
tests/testthat/interruptions/nested/between.gff
tests/testthat/interruptions/nested/map.syn
tests/testthat/interruptions/one-query-side/beside-exp-k2.txt
tests/testthat/interruptions/one-query-side/beside-exp.txt
tests/testthat/interruptions/one-query-side/beside.gff
tests/testthat/interruptions/one-query-side/map.syn
tests/testthat/interruptions/two-query-side/between-exp-k2.txt
tests/testthat/interruptions/two-query-side/between-exp.txt
tests/testthat/interruptions/two-query-side/between.gff
tests/testthat/interruptions/two-query-side/map.syn
tests/testthat/interruptions/two-target-side/beside-exp-k2.txt
tests/testthat/interruptions/two-target-side/beside-exp.txt
tests/testthat/interruptions/two-target-side/beside.gff
tests/testthat/interruptions/two-target-side/map.syn
tests/testthat/inverted-extremes/extreme-exp.txt
tests/testthat/inverted-extremes/extreme.gff
tests/testthat/inverted-extremes/map.syn
tests/testthat/io/long-exp.txt
tests/testthat/io/long.gff
tests/testthat/io/map.syn
tests/testthat/irregular-overlaps/left-exp.txt
tests/testthat/irregular-overlaps/left.gff
tests/testthat/irregular-overlaps/map.syn
tests/testthat/irregular-overlaps/right-exp.txt
tests/testthat/irregular-overlaps/right.gff
tests/testthat/multi-block/a-exp.txt
tests/testthat/multi-block/a.gff
tests/testthat/multi-block/b-exp.txt
tests/testthat/multi-block/b.gff
tests/testthat/multi-block/c-exp.txt
tests/testthat/multi-block/c.gff
tests/testthat/multi-block/d-exp.txt
tests/testthat/multi-block/d.gff
tests/testthat/multi-block/e-exp.txt
tests/testthat/multi-block/e.gff
tests/testthat/multi-block/f-exp.txt
tests/testthat/multi-block/f.gff
tests/testthat/multi-block/g-exp.txt
tests/testthat/multi-block/g.gff
tests/testthat/multi-block/h-exp.txt
tests/testthat/multi-block/h.gff
tests/testthat/multi-block/i-exp.txt
tests/testthat/multi-block/i.gff
tests/testthat/multi-block/j-exp.txt
tests/testthat/multi-block/j.gff
tests/testthat/multi-block/map.syn
tests/testthat/off-by-one/a-exp.txt
tests/testthat/off-by-one/a.gff
tests/testthat/off-by-one/map.syn
tests/testthat/one-block/hi-exp.txt
tests/testthat/one-block/hi.gff
tests/testthat/one-block/in-exp.txt
tests/testthat/one-block/in.gff
tests/testthat/one-block/lo-exp.txt
tests/testthat/one-block/lo.gff
tests/testthat/one-block/map.syn
tests/testthat/one-block/within-exp.txt
tests/testthat/one-block/within.gff
tests/testthat/one-interval-inversion/between-exp.txt
tests/testthat/one-interval-inversion/between.gff
tests/testthat/one-interval-inversion/map.syn
tests/testthat/one-interval-inversion/over-exp.txt
tests/testthat/one-interval-inversion/over.gff
tests/testthat/overlap/map-1.exp
tests/testthat/overlap/map-1.syn
tests/testthat/overlap/map-10.exp
tests/testthat/overlap/map-10.syn
tests/testthat/overlap/map-11.exp
tests/testthat/overlap/map-11.syn
tests/testthat/overlap/map-2.exp
tests/testthat/overlap/map-2.syn
tests/testthat/overlap/map-3.exp
tests/testthat/overlap/map-3.syn
tests/testthat/overlap/map-4.exp
tests/testthat/overlap/map-4.syn
tests/testthat/overlap/map-5.exp
tests/testthat/overlap/map-5.syn
tests/testthat/overlap/map-6.exp
tests/testthat/overlap/map-6.syn
tests/testthat/overlap/map-7.exp
tests/testthat/overlap/map-7.syn
tests/testthat/overlap/map-8.exp
tests/testthat/overlap/map-8.syn
tests/testthat/overlap/map-9.exp
tests/testthat/overlap/map-9.syn
tests/testthat/simple-duplication/between-exp.txt
tests/testthat/simple-duplication/between.gff
tests/testthat/simple-duplication/map.syn
tests/testthat/tandem-transposition/beside-exp.txt
tests/testthat/tandem-transposition/beside.gff
tests/testthat/tandem-transposition/map.syn
tests/testthat/tandem-transposition/within-exp.txt
tests/testthat/tandem-transposition/within.gff
tests/testthat/test-basic.R
tests/testthat/test-k.R
tests/testthat/test-relate.R
tests/testthat/test-rsynder.R.R
tests/testthat/test-util.R
tests/testthat/two-block/between-exp.txt
tests/testthat/two-block/between.gff
tests/testthat/two-block/hi-exp.txt
tests/testthat/two-block/hi.gff
tests/testthat/two-block/lo-exp.txt
tests/testthat/two-block/lo.gff
tests/testthat/two-block/map.syn
tests/testthat/two-interval-inversion/beside-exp.txt
tests/testthat/two-interval-inversion/beside.gff
tests/testthat/two-interval-inversion/map.syn
tests/testthat/two-interval-inversion/spanning-exp.txt
tests/testthat/two-interval-inversion/spanning.gff
tests/testthat/two-interval-inversion/within-exp.txt
tests/testthat/two-interval-inversion/within.gff
tests/testthat/unassembled/adj-hi-exp.txt
tests/testthat/unassembled/adj-hi.gff
tests/testthat/unassembled/adj-lo-exp.txt
tests/testthat/unassembled/adj-lo.gff
tests/testthat/unassembled/hi-exp.txt
tests/testthat/unassembled/hi.gff
tests/testthat/unassembled/lo-exp.txt
tests/testthat/unassembled/lo.gff
tests/testthat/unassembled/map.syn
tests/testthat/unassembled/tgen.tab
vignettes/.build.timestamp
vignettes/algorithm.Rmd
vignettes/intro.Rmd
vignettes/synder.bib
vignettes/yeast.Rmd
vignettes/yeast.tree
